You can go direct into the GPIO, will need to use hardware or software pull ups, or if the water meters output a voltage pulse you may need to reduce it to 3.3 volts max. I am using a pi on my boat which monitors (among a host of other stuff) two engine tachos. The tacho pickups are magnet/hall effect sensors, they output a pulse per revolution. I use interrupts to time each pulse. I see no reason this wouldn’t work for three pulse inputs. See wiringpi.com for ideas on programming.